Search for Variation information by Variation ID:
Detailed information for vg0817805780:
| Variant ID: vg0817805780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17805780 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTCCATTCCAGGATCTTGTCTGGTTGCTCCTCAAGAACAACAAAGACTGGATCCAAATTTTCTATCTGAAGATAGAACCACCTCGCTCGCCATTTGCTA[C/T]
GAGAAGAGGGGCACTGGAAGGGGATGTATCGCGACTTCAGGCCATCCCGAAGTCGGAAACCGACACATCCGGACACCTTTTTAGGTTCCATCCAGCACAA
Reverse complement sequence
TTGTGCTGGATGGAACCTAAAAAGGTGTCCGGATGTGTCGGTTTCCGACTTCGGGATGGCCTGAAGTCGCGATACATCCCCTTCCAGTGCCCCTCTTCTC[G/A]
TAGCAAATGGCGAGCGAGGTGGTTCTATCTTCAGATAGAAAATTTGGATCCAGTCTTTGTTGTTCTTGAGGAGCAACCAGACAAGATCCTGGAATGGACC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.10% | 4.90% | 9.99% | 2.07% | NA |
| All Indica | 2759 | 93.70% | 0.10% | 2.83% | 3.30% | NA |
| All Japonica | 1512 | 62.90% | 13.40% | 23.41% | 0.26% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 97.00% | 0.00% | 2.52% | 0.50% | NA |
| Indica II | 465 | 94.80% | 0.60% | 2.80% | 1.72% | NA |
| Indica III | 913 | 91.00% | 0.00% | 2.85% | 6.13% | NA |
| Indica Intermediate | 786 | 93.80% | 0.10% | 3.05% | 3.05% | NA |
| Temperate Japonica | 767 | 88.70% | 2.00% | 9.26% | 0.13% | NA |
| Tropical Japonica | 504 | 30.80% | 27.60% | 41.27% | 0.40% | NA |
| Japonica Intermediate | 241 | 48.10% | 20.30% | 31.12% | 0.41% | NA |
| VI/Aromatic | 96 | 56.20% | 20.80% | 22.92% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 3.30% | 17.78% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817805780 | C -> T | LOC_Os08g29080.1 | missense_variant ; p.Arg144His; MODERATE | nonsynonymous_codon ; R144H | Average:11.991; most accessible tissue: Callus, score: 32.629 | benign  |
0.087 |
TOLERATED | 0.12 |
| vg0817805780 | C -> DEL | LOC_Os08g29080.1 | N | frameshift_variant | Average:11.991; most accessible tissue: Callus, score: 32.629 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817805780 | 2.70E-06 | 1.56E-07 | mr1676_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |